Faded Memories
by NekoShard
Summary: What if Slash and Destroy had not ended so well? It didn't in here; Donnie got captured by the Foot and was given to Bishop! Now, with no memories, his body altered, and lies implanted in his mind, turning him against his family, will Donatello ever remember who he truly is on his own, or is it up to the combined efforts of Raph and April to bring his faded memories back to light?
1. Chapter 1

Faded Memories

Chapter 1

**Alright, this is my first TMNT fanfic so be merciful in the reviews. No flames if you please! Disclaimer: I do not own TMNT (Why would I be writing fanfiction if I did?)**

**Raphael's POV:**

"Spike, NO!" I cried, my arm still reaching out for my former pet, even though he had already hit the ground five stories below. Spike, I refused to think of him as "Slash," lay motionless on the cracked sidewalk. Tears pricked at my eyes, but I blinked them away and turned to help Leo up.

"You okay?"

Leo nodded slowly, "Yeah…You?"

I shrugged, "I'll be alright."

Seeing the question in my brother's eyes, I was glad of the excuse to turn away at the sound of approaching footsteps. Mikey stumbled over to the two of us, wincing due to his multiple cuts and bruises, his right hand clutching his upper plastron, nursing what had to be a broken rib or two.

"H-hey…Where's Spike?" He asked weakly.

"That was Spike?!" Gasped Leo, dashing over to the side of the roof.

"We'll fill you in later dude…"

I joined Leo at the edge of the roof where he was looking over the edge, his brows knit in confusion.

"Raph…What happened to Spike?"

I looked at my brother in amazement. "What are you blind? Can't you see Spike fell from the roof and is laying right…there…What?!"

The sidewalk was empty and the only indication that Spike had been lying there was the shell shaped crater of cracked pavement.

Leo looked grim. "This isn't good. Let's get out of here. Come on Mikey, Don-"

He broke off as we all realized that Donnie wasn't on the roof with us.

"Where-?"

"No idea," I said with a shrug. "he and Mikey jumped on Spike to keep him from hurting me, but after that I lost track of him."

I burned with shame at yet another time I had shown that I would not make a good leader for our team. Leo turned away to examine the rooftop before commanding,

"Spread out and search, but stay within earshot and sight of each other. We'll do this one roof at a time."

We scattered, searching every door, behind every object, and within every shadow, but there was no sign of Donnie. It was like he had vanished into thin air!

I returned to where Leo stood in the center of the flat roof, his eyes serious and concerned.

"Where's Mikey?" I growled before yelling: "MIKEY!"

"Shh!" Hissed Leo, clapping a hand over my mouth. "Do you hear that?"

Now that everything was silent, I could hear a faint sound coming from the ally to our right. Crying.

Not waiting for Leo, I raced down the fire escape to the ground. It was dark in the alley and I had to squint while my eyes grew used to the inky shadows. When I could see, I could make out a figure at the back of the alley. Mikey was on his knees, shoulders shaking from ragged sobs. He turned streaming eyes on me and choked out:

"R-Raph!"

"What's wrong Mikey?" Came Leo's voice from behind me. He moved forward to crouch by my baby brother and let out a cry of horror unlike anything I had ever heard him make. I roughly shouldered my way between them and my heart seemed to freeze in my chest.

Lying on the pavement was Donnie's bo staff, snapped in half jaggedly. The blade that usually was never out; was broken in half and slick with fresh blood as was the surrounding ground. A faint gleam caught my eye at the edge of my vision and I turned to see that the wall had three deep lines gouged into it. Drying blood was dripping down and filling the gashes, giving them the appearance of an open wound. I swallowed hard as I felt my stomach lurch.

Rage boiled up inside me and I clenched my hands into tight, shaking fists as I struggled to keep my tears from falling.

"Slash…" I growled. The truth that I had not wanted to see had practically punched me in the gut and I had no choice but to accept it as reality. Spike was gone and in his place was a warped, sadistic monster who enjoyed seeing others in pain and would kill and manipulate people who trusted him to exact some twisted form of revenge.

Looking down, I opened my hand to reveal the strip of purple fabric I had retrieved from Slash during our battle. Donnie's mask… That traitor had either killed or kidnapped my little brother and, in a way, it was all my fault. I got mad and took the mutagen, I left Spike alone with it, I spilled my feelings to him whenever I was angry, and I was too blinded by my temper and excitement to see Slash's true goal before he hurt my family. I had failed them.

I felt a hand on my shoulder and another pair of arms wrap around me as Mikey hugged me for all he was worth. I looked up into Leo's sapphire eyes. They were wet with unshed tears and his voice shook as he said,

"L-Let's go Raph. We-we have to tell Master Splinter what happened."

I looked at him in disbelief. Our brother is missing, possibly dead, and Leo wanted to play the perfect son and waste time going to explain everything to Splinter?

"No," I jerked away from my brothers and glared at Leo. "No. You tell Splinter what happened, Oh _Fearless Leader_!" I spat those words like they were an insult. "_I'm_ going to keep looking for Donnie. That's what _real_ brothers are supposed to do."

I turned and climbed the building to the roof once more, running away at top speed. Leo was calling desperately for me to come back, but I ignored him. I wasn't really thinking as I ran, but one thought was seared into my mind, both a purpose, and a prayer.

"_Find Donnie, find Donnie, Oh God, help me find my little brother!"_

**How did I do? I role play as Raph every now and then so he is probably the only one I will ever do in first person and this might be the last first person I will ever do in this story. Well, leave me reviews! Those are like oxygen to me when it comes to writing. **


	2. Chapter 2

**NekoShard: **_**Hello everyone! Thanks to everyone who reviewed, it made me really happy! I also want to give a shout out to my friend ZaneDonnieluver who helped me a lot with the overall plot of this story. It may never have been published otherwise!**_

**Raph: **_**"Can we get on with this? I want to know what's happened to my brother!"**_

**NekoShard: **_**"Sure thing. Here is the disclaimer: I don't own TMNT!"**_

**Raph: **_**"Thank God…"**_

**NekoShard: **_**"HEY!"**_

Donatello woke up when he was dropped onto a cold stone floor. The back of his head made a sickening crack when it made contact with the hard ground. Spots of light swam in front of his eyes and his head spun dizzily. The left side of his face felt as though someone has branded him with three rods of hot metal and was stiff with drying blood. A blurred, confused murmur of voices was all around him, but his hearing was fuzzy and he could not make out any words. He could only assume that they belonged to his family.

"Guys what-ugghnn!" His words were cut short by a cruel, well-placed kick to his side where he was not as protected. As Donnie doubled over, retching in an attempt to replace the oxygen that had been forced painfully from his lungs, a high voice called in a cold, almost bored tone,

"Bring it to me."

A large scaly hand seized his left arm and dragged him roughly forward. An involuntary cry of pain escaped him as agony lanced up his arm. It was only then that he remembered his broken arm and what had led to his capture.

**Flashback**

_Donnie leaned back against the edge of the roof and tried to catch his breath. Mikey was lying unconscious a few feet away and Raph was battling Slash, defending Leo. Donnie couldn't see everything, but he heard a sudden cry of anguish from Raph as he called the name of his old friend. Donnie made an attempt to sit up, but his arm, even though it was in a crude sling, gave a painful twinge and halted his movements. His vision swam. A faint noise came from behind him and he grabbed his bo staff to support himself as he stood up. A hand grabbed him around the neck and jerked him off the roof. Donnie was jerked around to face a battered Slash. Opening up his mouth to yell for help, Donnie jabbed forward with his nagita blade catching Slash in the shoulder. With an enraged growl, the larger turtle raked his claws down the left side of Donnie's face before jerking the blade from his shoulder, breaking the blade, and snapping the staff in two. Then Donnie blacked out._

**End of Flashback**

Donatello was relieved to be dropped again. Even though it was rough, it relieved some of the pressure in his arm. He remembered that Raphael had set and bound up the arm in a sling, but Slash must have undone that to cause more pain.

"_It certainly worked…"_ Donnie thought weakly. _"Just remember to keep the arm still and-"_

His thoughts were cut off as someone grabbed him by the front of his plastron and his head was forced back by the tip of a slim blade. Karai's cruel eyes burned into his.

"So…Donatello. It's a pity that Slash did not bring me a greater prize than you, but I can still find a way to make use of your sorry existence."

With a glare, Donnie muttered, "I'll never work with you."

"You don't have a choice, you are mine to do with as I please."

"What?"

Karai's gaze flicked briefly to one side and Donnie followed it. Slash was standing to one side, his rough face cast into eerie shadows. Then Donnie understood. Raph's former pet had turned him in to gain a position in the Foot Clan!

Looking thoughtful, Karai mused, "Now what should I do with you? Leo was the one that I really wanted. I could use you as bait but it is very likely they will manage to rescue you and stop me, something they do with irritating frequency. I really have no use for you though…Tell me, what do you do with something that you don't want anymore?"

Donnie swallowed hard, his mouth dry, as she continued, "You give it to someone who will use it more."

A man stepped from a shadowed corner by the dais. He wore a dark, pristine suit and stylish sunglasses that completely hid his eyes. His mouth was set in a cold, grim line.

Karai smiled and threw Donnie to the floor again. He landed on his injured arm, but swallowed the yelp of pain that rose in his throat.

"Meet Agent Bishop. I think that you two will get along very well. He enjoys taking things apart to see how they work."

Donnie coughed hard, spitting up blood before saying defensively, "I only create, I never destroy if I can help it."

Karai gave him a sharp kick again as she said cuttingly, "That explains the pathetic weapon that you used to use. Bishop, take him. He's all yours."

In a desperate bid for freedom, Donnie shoved himself to his feet and ran, hoping to get close to the wall so he could climb out of reach and hopefully gain an uphill advantage. He ducked and dodged Foot robots as well as Xever and a terrifyingly enraged Rahzar, trying to avoid a fight wherever possible to protect himself from further injury since he was in no condition to fight.

Suddenly, Donnie felt a sharp prick on his upper arm. Halting with surprise, he looked down to see the feathered end of a tranquilizer dart protruding from his olive green skin. He plucked it out and glanced over to where Bishop stood, still pointing the weapon at him. It was as if time had frozen. Then Donnie swayed dizzily, dropping to his knees and trying frantically to remain awake, but in the end, he collapsed unconscious on the stone floor.

Bishop knelt by Donnie's unconscious body, examining him briefly before gesturing to two heavily armed men who were standing by the door. They came forward and picked up the adolescent mutant and began carrying him out to a waiting truck none too gently. Addressing Karai Bishop said,

"If what you told me about this turtle is true then he should be perfect. Expect the merchandise by the end of this month."

He dropped a small metal object into the kunoich's hand and began to walk away, his overcoat billowing behind him.

"As agreed."

**Raph: **_**"WHAT?"**_

**NekoShard: **_**"What?"**_

**Raph: **_**"You can't just stop there!"**_

**NekoShard: **_**"Uh yes I can."**_

**Raph: **_**"Why?"**_

**NekoShard: **_**"Because you tied me to a chair for messing with your family! Besides, I think this seems like a good stopping point for right now."**_

**Raph: **_**"Grrr…You readers better review and fast! Otherwise this family is never going to get back to normal!"**_


	3. Chapter 3

NekoShard: _**"Hello my dear readers! Thanks a million for the fantastic reviews! ***__**Looks through the reviews***__** "Oh, Raph, Emmius99 says hello to you. "**_

Raph: _**"Who the shell is that and why do I care?!"**_

NekoShard: _**"You care because she is one of the reviewers who spurred me to get this chapter written and posted before the month was over!"**_

Raph: _**"Oh…Uh, Hey Emmius! Nice to meet you…"**_

NekoShard: _**"Much better. Enjoy the next chapter!"**_

Harsh florescent light beat down on Donatello. He tried to open his eyes, but it seemed that only one opened fully. Looking up, Donnie saw that the light came from some sort of grate above his head and he sat up quickly, rubbing his eye to clear it. Immediately his arm felt as though a lance had been thrust through it and his head spun, the three gashes on his face throbbing. Wincing, Donnie swung his legs over the edge of the low cot and set them on the cold floor, noticing as he did so that the entire room was made from highly polished steel. Getting up, he limped over to the opposite wall and gazed at his reflection with a sense of everything being unreal. His gear was gone. Mask, knee and elbow pads, T-phone, weapon, even the bandage-like wrappings that had been around his wrists and feet were missing. The reason why his eye would not open fully was because the blood had dried over it, sticking it shut and making half of his face a rust colored mask.

Suddenly, footsteps sounded above his head. Donnie fell to the ground, trying to cover his ears while only having one functioning arm. He realized that the room he was in was both a holding cell and a torture chamber. The metal walls and roof created a sort of drum that vibrated the occupant and caused extreme pain from the crashing noise that was a result from people walking overhead. He gritted his teeth and silently willed the noise to stop. To his surprise, it did. A faint clatter reached Donnie's ears as the grate above him was removed and a folding ladder was put down. Getting the idea, Donnie began to climb slowly due to his hurt arm. A man looked down at him and made a noise that indicated impatience, grabbed him roughly by the arm and dragged him the last foot or so before dropping him on the floor with an expression of distaste. As Donnie got shakily to his feet, the barrel of a gun bumped against the back of his head where skull and spine met and the man snarled,

"Get moving, freak. And don't even think about trying to escape; I'll put a bullet through this thick head of yours before you make it three yards."

Donnie swallowed and nodded in understanding. He was shoved forward and began walking, turning whenever a rough nudge from the gun directed him to. His eyes darted back and forth, learning the hallways, doors, and anything else that might offer him assistance in an escape. A harsh smack of a rifle against his shell distracted him as one of the other guards snapped,

"Keep your eyes on the ground mutant!"

Donnie looked at him with eyes that showed no anger, only disappointment. The man seemed unnerved for a moment but covered it with anger, striking Donnie across the face with his hard leather gloved hand. The olive green skin on his cheek split and warm blood trickled from the cut as the man grabbed him harshly by the shoulders and leaned in, his breath hot and stinking of cigarettes as he hissed,

"Don't you ever look at me like that again you piece of scum! I will personally kill you if you do, no matter how valuable you are. Now get moving; Bishop's waiting."

A couple minutes later, Donnie was shoved through a door and against a wall. Manacles were clamped around his ankles and wrists, tightened till they hurt. He could move forward about a yard, but no further. The guards then left, closing the door and extinquishing all light in the room. There was utter silence for a while and Donnie struggled to keep his breathing even and himself calm.

"Welcome to my laboratory, Donatello," Said a smooth, deep voice. Bishop walked out of the shadows, his face. "I daresay that it is far more advanced than your own; many more ways to learn what "makes you tick."

Donnie shuddered, "What do you want with me?"

Bishop walked over and turned on a light, illuminating a large room filled with an uncountable number of alcoves. Donnie's eyes widened in shock and horror as he saw that each one of these niches contained a figure that resembled a human with snake scales standing stiff and at attention. At first glance they appeared to be some strange form of decorative statuary, but closer examination revealed that they were breathing slowly and evenly, as if in a deep sleep. Many tubes were attached to each figure, oxygen masks covered their mouths, and sturdy restraint bands secured their arms and legs against the wall.

Reading Donnie's shocked expression, Bishop said coldly, "They are alive, but their brains do not yet function properly. They are to become an elite squad of warriors that will be employed to do the dark, dirty, and less legal of the government's jobs."

Bishop carelessly examined a short surgical knife before setting it on the lab table and reaching over to straighten out one of the many syringes that lay color-coded on a tray as he continued to speak.

"I assume that you are familiar with the Star Wars movies? If you recall, the clone troopers were created to be able to fight immediately. I adopted the same policy with these experiments. Unfortunately, I could not create an intelligence that would allow for anything more than the basic functions of the body to be maintained in a state similar to a coma. I decided that they had to be given an existing intelligence boost from someone else for them to be complete. However, I did not wish to use any of the men under my command because the circumstances that these troops would be put into would require more intelligence than those men possess. I had no one I could use until Karai managed to contact me. She gave me the information about you and your brothers a bit at a time, but in the end, I decided that you would work the best for this experiment. That, Donatello, is what I want from you."

At those words, Donnie was jerked off of his feet as the chains on his wrists and ankles went taught and retreated into the wall as a flat, tilted slab of metal moved forward. Donnie felt his shell press against it and stiffened with horror as metal restraint bands secured him and held his head in place. Walking over to his prisoner, Bishop casually primed a large, lethel looking needle as he explained,

"Your mind has a very clear understanding of tactics and the natural world. I can make good use of that. By extracting some brain fluid and tissue I can give my test subjects a high intelligence while stabilizing the lower level mutation I created them with."

Raising the needle, Bishop squinted down it as if he were sighting down the barrel of a gun as he said coldly,

I believe that it is only fair to warn you that this will hurt. A lot. In case you do not make it through the extraction, know that science thanks you for your sacrifice, Donatello."

The needle descended. Donnie's eyes widened and his pupils contracted to pinpoints as he screamed in agony.

Thirty minutes and many vials of "intelligence" later, Bishop sent the liquid flowing through the various tubes and into the hundreds of test subjects. He watched as they opened their eyes one by one, looking around them with expressions of mild curiosity. Bishop smiled grimly and glanced behind him at where Donnie slumped senseless against the upright table, supported only by the restraint bands.

"Over two hundred new troops are ready to begin their work. Now all they need is a leader…"

NekoShard: _**"Whew! That was intense for me to write!"**_

Raph: _**"I asked for reviews so you could make things better, not worse!"**_

NekoShard: _**"Yes, but things almost always have to get worse before they get better and the same is true with this story."**_

Raph: _**"I hate you so much…"**_

NekoShard: _**"Just keep telling yourself that; we both know that's not true."**_

Raph: _**"You stay here any longer and I'll show you how true it is."**_

NekoShard: _*****__**Gulp**__*** "Uh, please review everyone! Okay, okay I'm going!"**_


	4. Chapter 4

NekoShard: _**"Yay! More reviews!"**_

Raph: _**"…This had better be an improvement from the last chapter."**_

NekoShard: _**"We'll see. Let's get on with the story!"**_

Back in New York, the Hamato Clan was in complete disarray and depression. Every night, Leo, Raph and Mikey patrolled the streets both in the heart of and around the suburbs of the city. April kept here eyes and ears open for any information during the day and snooped around on the weekends.

In the lair, Leo drowned his sorrows and guilt in near ceaseless training, while Mikey played video games, but usually did more staring blankly at the screen than actual playing. Master Splinter kept the broken pieces of his son's staff on a low table in his room and meditated before them constantly, barely pausing to eat or sleep in the hopes of somehow meeting his child on the astral plane. Raph wandered the sewers aimlessly, finding little joy in beating up his punching bag or sleeping the day away in his room. Whenever he was home, he spent all his time in Donnie's laboratory, looking at various machines and inventions that were either being worked on or had yet to be started.

Today was no different. Raph silently walked into his brother's lab and closed the door behind him. He walked over to one of the worktables and ran a hand absentmindedly over the tools, worn smooth in places where Donnie had held them so many times. A sad smile touched Raphael's face as he saw the scorched, partly melted toaster sitting on a shelf where it could be quickly taken down and worked on. A purple sticky note was stuck on the side and read: _Note to self, try and find nichrome wire as an alternate heating element to the bimetallic strips. Also find a way to prevent oxygen from reaching the heating elements; less chance of an explosion the next time Leo uses it._

With a sigh Raph moved on. He wanted more than anything to have some proof that Donnie was alive, but could think of no way for that to happen. Suddenly he remembered something that Splinter had told him when he was younger.

"_Meditation is not just a way to calm one's spirit, Raphael. It is a way for us to occasionally commune with our loved ones while we are separated from each other."_

Raph's mind was made up. He grabbed an oil-smeared tarp from a corner of the room, and spread it out on the floor. He sat down upon it in the lotus position and closed his eyes, trying to let his mind go blank and his breathing even. He sat still for what felt like hours with no results. Exasperated, Raph gave up and opened his eyes, only to let out a cry of surprise. The laboratory had vanished and was replaced with an empty black void. In the distance however, a faint purple light shone. Standing, Raph made his way towards it, slowly at first, but then increasing his speed. He could sense a familiar presence at the center of the light.

"Donnie?"

"Raph?" Cried a voice. The light dimmed and Raph could see Donnie standing before him, looking startled and confused.

Grabbing him in a hug, Raph cried, "You're alive!"

Donnie smiled weakly, "Y-yeah…I suppose that I am."

Stepping back, Raph said seriously, "Do you know where you are right now? I'll tell the others and we can come to bring you home."

"What?" Donnie's gaze was distant and confused.

"Where are you right now?" Asked Raph again, speaking more slowly. "When Slash kidnapped you where did he take you?"

"I was…captured?" Asked Donnie. "I…don't remember…"

Frightened now, Raph pulled out a wild card.

"_April_ is really worried about you, we all are!"

"Who's April?" Asked Donnie, he seemed nervous now and began to tremble slightly. Desperate, Raph grabbed him firmly by the shoulders and yelled,

"LOOK AT ME! Look and tell me who you are!"

Now Donnie seemed terrified, he jerked away and put his hands to his head muttering to himself his eyes dark with fear.

"_Who am I?_

_I am Hamato Donatello; Donnie._

_I am a scientist, medic, techy, ninja, friend, confidant, brother._

_Right?_

_Something is inside my mind…It is sucking, tearing my memories to shreds…_

_It's turning me…I don't want to lose myself…_

_I've always been different, and I like that._

_I enjoy being the geek, the bookworm, the hopeless romantic._

_I shouldn't change, I don't want to, but it's making me…_

_I need to hold on, tell myself who I am._

_I am a ninja…or was I?_

_Everything is so confused and jumbled_

_Raph, Leo, Mikey, Splinter, April_

_Everything is so torn and fragmented…_

_Brothers, Father, Crush_

_Who are they?_

_No! Remember, hold on to them!_

_I know they are dear to me_

_But it is so hard to hold on to them."_

Raph was panicked and he called out to his brother in an attempt to snap him out of his mutterings. "Donatello!"

"_I hear you, but who are you?_

_The voice is familiar, like an echo from many long years ago…_

_I wish I could remember, but the monster in my mind has sharp claws_

_They are doing their duty, destroying my memories…"_

"Please little brother! Remember me! Remember the promise I made you as a kid! I'll always protect you; I'll always be there for you. That's what big brothers do."

"_He calls me brother but I don't know why…_

_The monster is full now, gorged on my life's memories._

_That voice...it asked me a question…_

_Who am I?_

_How do I answer…I have no name, no memories, no purpose for existing…_

_I am nothing…"_

Raph let out an anguished cry as Donnie murmured those final words. Darkness enveloped him once more. An impenetrable barrier arose between him and his brother.

"No. No, no, no! _DONATELLO!_"

A light flicked on, blinding Raph after the near complete darkness, and Master Splinter said gently,

"Raphael, calm yourself."

Turning, Raph punched the wall in rage and despair, feeling the skin on his knuckles split open and several bones break as warm blood dripped to the floor. Good. He deserved the pain and far more after he failed to protect his brother. After he broke his promise.

Raphael fell to his knees, fighting back the tears that burned his eyes and choked up his throat. His father knelt before him and skillfully bound up his broken hand before drawing him close the way he had done when Raph was little.

"Let them flow, my son."

Under normal circumstances he would have pulled away, but now he held on to his father as if he were an anchor in the middle of a raging storm. Raph allowed the tears to roll down his face, soaking his mask as he sobbed in tortured grief.

"He doesn't know us!" Raph choked out. "I could see him, feel him slipping away and I just-just couldn't stop it!"

NekoShard: _**"…"**_

Raph: _**"…"**_

NekoShard: _**"Please review if you do not hate me…I swear it will get better in time!"**_


	5. Chapter 5

**Mikey:** _**"HEEEEEEEEYYYY PEOPLE! What's doin'?"**_

**NekoShard:** _**"Mikey that's Raph's seat! What are you doing in here?"**_

**Mikey:** _**"Leo took over the TV controls and is watching Space Heroes. So I thought I'd hang with you for a bit."**_

**NekoShard:** _**"Uh, well I don't think Raph is gonna be too happy about you taking his place…"**_

**Raph:** _**"You're right about that." ***__**Cracks knuckles**__*****_

**Mikey:** _**"Lemme at least do the disclaimer! NekoShard totally owns TMNT! HAHAHAHAHA!" ***__**Runs away**__*****_

**NekoShard & Raph:** _**"MIKEY!"**_

The teenager opened his eyes, blinking rapidly in the unnatural florescent light. The room smelled of cleaning chemicals. It was a harsh, uncaring, steril scent and stung his lungs. Sitting up, he raised a hand to his head, feeling bandages. Had he been in an accident? Turning his head to look around, he caught his reflection in the polished metal wall opposite his cot and let out a strangled scream of horror. The figure in the reflection had olive green skin, but its chest was covered in a tan plastron while a brown shell was on its back. The creature's head was humanoid but it lacked a visible nose and ears even though its deep brown eyes and mouth were very human-like. Its hands and bare feet had three digits each and bandages were wrapped around the top of its head. Its face was disfigured by three rows of stitches running vertically across the left side over its eye. Slowly, the teenager raised a hand to touch the stitches, watching as the figure in the makeshift mirror opposite him mimicked the movement. He began to hyperventilate.

"_What-what am I?"_

As much as he tried to suppress the thoughts, he could hear voices hissing and jeering at him, calling him names like freak, scum, mutant, _monster_. He uttered a choked sob and buried his face in his hands, trying to block the image of his reflection from his mind as he shuddered, revolted and disturbed.

Hinges sounded above him and he glanced up to see a folding ladder being let down. Two men descended and stood stiffly at attention. They looked as though they were on steroids with their huge muscles bulging as they held enormous machine guns in a way that suggested that they were perfectly capable at using them and would not hesitate to do so the moment he gave them cause.

"I am pleased to see that you are awake."

The mutant nearly jumped out of his shell in fright. He had not noticed the third man in the dark suit and black trench coat who had climbed down the ladder after the armed men. The man stood still, watching the prisoner from behind dark sunglasses before walking forward and drawing up a chair from the corner of the room to sit in front of him.

Shrinking back, the teenager said weakly, "Where am I, who are you, and more importantly, who am I?"

The man leaned back in his chair as he replied slowly, "You are in a top secret government base. I cannot give you the exact location for security reasons, but suffice it to say that you are safe. I am Agent Bishop, a government scientist. As for your backstory, I was hoping that you would provide me with more information on that subject."

"I-I have no memory of a time before my waking up here," Admitted the teenager uncomfortably. "Please tell me if you know anything."

Bishop was silent for a moment, then, "My men discovered you in a warehouse on the outskirts of New York City. Your arm was broken and you were being beaten up by three other people who could not be identified. My men rushed in to drive them off, but not in time to save you from a final blow. As your attackers fled, one of them took a three-pronged blade, a sai, and scored a hit down your face, giving you those wounds that will leave you scarred for life." Leaning forward, Bishop continued. "You were half dead from blood loss and exhaustion by the time you were brought to the base. It was touch and go for about a week as you were in a deep coma. However, you clearly are stronger than I anticipated and have awoken without complications. I am afraid however, that is all I know about you."

Bishop looked at his watch and stood quickly. "My apologies, but I have an urgent meeting that I must attend. I will continue to search for clues regarding your identity between the time of my next visit."

The prisoner watched sadly as Bishop and his men left and closed the hatch behind them. He hadn't really learned anything from the conversation; he still didn't even have a name or his own age.

"No name, no age, no purpose…I'm nothing."

He swallowed hard as he came to that realization, and accepted that as his current identity.

Weeks past while the teenager's injuries healed. He measured time by whenever Bishop came to see him, once a week, every Tuesday. After a while, he was allowed to go out, under supervision, and exercise, letting out pent up energy. Bishop received no new information on his prisoner's past, but he brought him a new book to read every visit. His favorite was the one about poisonous plants. They could seem so harmless, but one taste of the fruit and death was nearly inevitable for most. Fascinating.

One day, the mutant was sitting cross-legged on his cot, reading about a poisonous purple plant called nightshade, when Bishop entered the room, his face grave.

"I have news about your past."

He immediately had his prisoner's attention and continued with deliberate slowness.

"I discovered the true identities of the people who attacked you. They are mutants similar to your-self, calling themselves ninja. After a little more digging, I finally found out the truth. They are your brothers."

Getting up, the nameless teen moved forward in confusion. "That isn't possible! A family wouldn't…wouldn't try to kill their own flesh and blood."

Bishop said coldly, "They would. They are led by a mutant rat and they always listen to his orders. The rat would only need to hint that you should be gotten rid of, and they would obey. They live in a harsh, cold world and people like you, people who have good hearts, are a liability and must be eliminated. They were simply looking out for number one. You were not important enough to them. Now if you will excuse me, I have a meeting and you must want to be alone."

When Bishop exited the room, he turned around and stood still as he looked down upon his prisoner. Donatello didn't move for a while, but then he snatched up his book and hurled it against the wall. He lunged at the wall and punched it repeatedly in an insane rage. Tears were pouring from his eyes and a scream of rage and grief burst from him as he fell to his knees, clutching his head as if he were trying to will memories that would prove Bishop's words wrong to appear. When that didn't happen, he fell to the floor, sobbing bitterly. Bishop chuckled softly at his success and returned to his laboratory to prepare the second stage of his plan.

Miles away, in the sewers of New York City, Raphael stirred restlessly in his sleep as the tortured sobs of his lost brother echoed through his dreams.

**NekoShard:** _**"So it appears that Raph and Donnie have some type of weak mental link."**_

**Raph: **_**"So how does that work? What happens with that in upcoming chapters?"**_

**NekoShard:** _**"I have no idea! I make most of this up as I go."**_

**Mikey:** _**"Roll in the reviews people! The first five get a slice of my eternal pizza!"**_

**Raph:** _**"Is that offer supposed to make people want to review?"**_


	6. Chapter 6

**NekoShard: **_**"Reviews, reviews, reviews! I've never had so many coming in at once before, this is amazing!"**_

**Raph: **_*****__**Leans back and puts feet up on table***__** "Well you never had someone as charming and good looking as me asking people for reviews. How could they resist?"**_

**NekoShard: **_**"Or as humble…Well, on with the story!"**_

It had been three weeks since Bishop's revelation and he had not been to see his prisoner since then. He had sent orders to his men to keep the lights in the teenager's cell off at all times and to have no contact with him while feeding him the barest minimum to keep him alive. Now, with his lab ready, Bishop went to see the young mutant to forward the next stage of his plot.

As he descended the ladder, he allowed his hand to slip into his pocket and his fingers to curl around the handle of a small tranquilizer gun. Just in case. Standing still, Bishop gazed coldly into inky shadows, waiting for the prisoner to reveal himself. Suddenly a faint rustling sound came from behind him. Turning, Bishop saw his prisoner standing before him. He was much changed since his arrival, his olive green skin was abnormally pale, his body very thin and weak looking, but his eyes were where the change was most apparent. Where there used to be such trust, compassion, and curiosity, there was nothing more than sadness and a deep-seated hatred.

"Bishop. Tell me what to do; I'll work with you provided I get to kill my _"brothers"_ myself."

A slow, cruel smile spread across Bishop's face and he extended a hand to shake,

"I would be delighted to offer you just that chance."

As their hands clasped, Bishop added as if as an after thought,

"You will need to become much stronger than you are now if you ever wish to defeat your brothers-"

"Do not call them that," Snarled the haggard teen.

"Very well. I have told you already that I am a scientist. I can give you the strength you need as well as a form that will set you apart from those you face. They will never learn your true identity. Now come with me, we have a lot of work to do."

This time the prisoner walked to Bishop's lab of his own free will, unchained and eager to exact his revenge as soon as possible. A smile that looked more like a sneer crossed his face as he looked to Bishop for directions.

"Step into this compartment right here and remain still while I attach these tubes to you. They will help keep you healthy while the operation is underway."

The mutant narrowed his eyes with slight suspicion, "What exactly will you be doing to me in this "operation?" How can I be certain that you won't dissect me, you are a scientist after all."

Bishop continued to prepare several different knives, syringes, and a large machine as he replied smoothly, "Not losing your nerve are you? Don't worry, what use would I have for a dead mutant? However, I do not see any harm in describing what will be done to you."

A screen flickered to life and a full image of the teenager appeared.

"I was considering adding some aspects to you for additional balance as well as a built in weapon," Seeing the look of faint confusion on the subject's face, Bishop clarified. "I mean that I will give you a long, powerful tail."

He pressed a button on the keyboard and the appendage was added on the screen.

"I also decided to disguise you further by adding some spikes along the top of your head and the upper edge of your shell. Those could also act as protection for you. Finally, I intend to allow you greater freedom by letting you blend into the shadows. I will alter your skin color to make it darker. You will be unrecognizable."

Straightening, the prisoner said, "Very well, but I have a suggestion."

"Oh?"

Opening his hand, the mutant revealed a scrap of paper, "I've chosen a name for myself, now it is up to you to make me represent it."

Taking the paper, Bishop looked at the words upon it and gave a cruel smile.

Nightshade. Danger level: Lethal.

"Let's get started then."

The operation took a long time to complete as it had to be done in several stages and involved complex alterations of DNA and other such in-depth changes. Bishop did not take a break for another week, but in the end, Bishop had never felt more pride and accomplishment in any other work. He had enhanced Nightshade's eyesight, allowing him to see in the dark far better, given him sleek, powerful muscles, and a long tail had sprouted, rippling with muscle. His biggest change was the alteration of Nightshade's skin, shell, and eye color. His skin was now a purple that was several shades darker than his mask had been and his shell was a light shade of navy blue and matched the spikes that stuck up from his head. His eyes were now a glowing shade of yellow-gold.

The subject stirred slightly and his eyelids quivered. As he opened them, Nightshade appeared a bit confused as he raised his hands to look at them. Then he sat up in bed, his yellow eyes darting around the laboratory before they rested on Bishop.

"Welcome back to the world of the living," Smirked the scientist. "Are you ready for your mission to begin or will you need time to adjust to your new form?"

"I feel ready for anything!" Declared Nightshade as he leaped from his bed; the movement became far less graceful as he went sprawling on the floor, dragged off balance by the new weight of his tail. He got carefully to his feet and casually amended his statement.

"Although, a little bit of practice walking, jumping, and climbing may be in order."

Bishop's eyes hardened slightly, "I am afraid that you will have to learn on the fly. There is an important meeting that you and I must attend if you are to begin the destruction of your-attackers. I have armor for you to wear as protection during this mission. Put it on while we are on the plane."

"The plane?"

"Yes. We are going to New York City. It is time to begin the war."

**NekoShard: "Done! Whew this took a while for me to work out!"**

**Raph: "Yeah. At least it gave Mikey the time to get rid of that "eternal pizza." The living room was getting rank!"**

**NekoShard: "That Mikey…Well review everyone while I get started on the next chapter."**


	7. Chapter 7

**NekoShard: **_**"Hi everyone! I was reading the reviews and saw some people wanting to know what happens with the rest of the gang during the time Donnie is gone."**_

**Leo: **_**"What about us?"**_

**NekoShard: **_**"Oh hey Leo! I was just telling the readers that this chapter is showing what's happening in the lair while Donnie's gone. Care to sit in and read? Raph had a date with his punching bag."**_

**Leo: **_**"Sure, let's get started!"**_

April O'Neil walked down the long abandoned tracks that lead to her friend's secret home. She had just gotten out of school and had called off yet another "study session" with Casey. She had neglected her ninja training as of late and had not seen her friends either; they had all been trying to deal with losing Donnie. Tears stung her eyes but she brushed them away. She had reached the entrance to the lair and didn't want to make her friends feel any worse. Walking into the living room, April saw Mikey crashed on the couch, his fingers a blur as he worked his way through a level on some violent video game.

"Hi Mikey!" April said cheerfully, "How's the new game coming?"

Mikey looked up at her, his face sober and eyes sad as he replied, "It's fun, I'm already on level thirteen."

April smiled slightly, "Nice! I only gave that to you a month ago and it took me three months to get that far when I first played it."

"Mhm…" Mikey had turned back to the screen, keeping his face hidden from sight. Getting the message, April turned and walked towards the dojo. She glanced back briefly and saw that the orange masked turtle had leaned forward, his head in his hands. His avatar had just been defeated and the words "GAME OVER" flashed red across the screen, but Mikey didn't seem to notice. His shoulders were shaking, and April knew that he was crying.

The dojo was empty when she entered it, but April felt a strange sense of peace well up in her. Something about this room felt timeless and unchanging, as if a deep peace resided there that couldn't be shaken. She breathed in deeply, smelling the incense that hung in the air. Suddenly, a sliding door that led to Master Splinter's room opened up and Leo exited, making sure to carefully close the door quietly behind him.

"Leo, where is Master Splinter?" April asked quietly, "We were going to continue my training today."

Leo looked calm and casual, but his brow was slightly furrowed with worry as he said, "Sorry April, but Sensei is resting right now. He's been spending all his time meditating trying to find out more about Donnie and hasn't been taking care of himself the way he should. I finally convinced him to get some sleep just now. If you want I could help you practice what Sensei has already taught you; that way your visit won't have been a total waste."

April nodded in agreement and the two faced off. She had sparred with Leo a few times before, but had never beaten him. It had helped her sharpen her skills though and she enjoyed fighting with the eldest of her mutant friends. This time around however, Leo did not seem as focused. His punches were easy to deflect, his moves predictable, and his footwork sloppy. It wasn't long before April had tripped him and Leo crashed to the floor. He began to get up so they could continue, but the kunoich in training dropped to her knees beside him and said gently,

"We don't have to keep going, Leo. I can see you are under a lot of stress."

The turtle's calm face changed to show the sadness, fear, and responsibility that he had been trying to hide and his shoulders slumped, "Is it that obvious?"

April smiled sadly and put a hand on his arm, "Don't worry, no one thinks any less of you for being sad and tired."

Leo bowed his head and closed his eyes as he muttered, "It's not just that…I failed as a leader and as a brother. Don't deny it!" He snapped as April opened her mouth to disagree. "I should have been there to protect him! I'm the leader of this team and I should have been watching out for Donnie and not chasing down the mutagen because of my stupid pride. Raph was at least trying to stop Slash! I'm a sad excuse for a brother."

_**SMACK**_

Leo raised a hand to the throbbing welt on his cheek and stared at April in shock. Tears glimmered in her eyes as she glared at him and cried, "Don't ever say that Leo! It was not your fault! It wasn't any of your guys' faults! Donnie wouldn't want you guys beating yourselves up because of him, would he?"

Leo blinked and stood up.

"You're right April, I was being stupid. I'm sorry."

A laugh rang out from the doorway and the two of them turned to see Raph leaning against the doorframe.

"Nice one April! I'd never have guessed that you had it in you, but you managed to slap some sense into Leonardo here. Literally!"

He grinned cheerfully and walked over, extending his hands and helping his friend and brother to their feet.

"So, Leo," Raph said. "I was wondering if I could borrow one of your books. You know, the one about this kid named Eragon and his dragon. I've been looking to do some reading lately."

April gaped at Raph in astonishment, she had never seen the normally hot tempered and often, moody turtle act so…Mikey-like. Leo however took this Raph in his stride and nodded.

"Sure. It is on the third shelf in my room on the top at the far left. Start with the blue book, "Eragon." If you like it then you can come back for the others."

"Thanks bro!" said Raph, giving him a friendly slap on the shell. He gave April an awkward, one armed hug and then left the room calling over his shoulder as he did so: "Come over again soon 'kay April? I'll spar with you next time!"

The red head looked over at Leo in confusion and he answered her with a sad smile.

"He's been that way for a while now. A couple of weeks ago Raph and Sensei shut themselves in a room for a long time. When Raph came out his hand was bandaged and broken, but he was acting cheerful like you just saw."

Leo looked after his brother and said slowly, "I never understood this saying before, but now I think that I do. "The people who hurt the most; smile the brightest." That's what's going on with Raph…"

Later that night, April was still thinking about Leo's words. She was ready for bed and her lights were off, but she was restless. She flicked on the radio and walked out onto the fire escape outside her window and sat down. Memories swirled through her mind, ranging from the first time she had met Donnie, when he had saved her from the Kraang, to the last time she had seen him. When she had gotten mad and yelled at him that she didn't want to see him again. Now April wished more than anything that she could take back those words. She sighed sadly and leaned back against the wall, hugging her knees to her chest. The radio was playing the song "Airplanes" and she let herself get caught up in the music for a moment.

"_Can we pretend that airplanes in_

_The night sky are like shooting stars?_

_I could really use a wish right now;_

_A wish right now, wish right now._

_Can we pretend that airplanes in_

_The night sky are like shooting stars?..."_

Tears fell from April's eyes as she gazed up at the sky. The stars were covered by clouds and pollution from the city, but as she watched, a sleek business jet roared over her house, headed for a private airport. April wished so hard that her best friend was simply on a trip and imagined that that very plane was bringing him home. But at the same time she knew it was impossible, and as the song ended she buried her face against her knees and whispered softly,

"_I could really use a wish right now…"_

**NekoShard: **_**"Well I hope this is okay, I really stink at writing April."**_

**Leo: **_**"Don't worry about it Neko, you did fine!"**_

**NekoShard: **_**"That's up to the reviewers. Please review everyone!"**_


	8. Chapter 8

**NekoShard: *****Is sitting in her room with the lights on*******

**Raph: *Turns the lights off* "Hey! Who turned out the lights?"**

**NekoShard: "AAIIIIIII! TURN THOSE BACK ON NOW!"**

**Raph: *Is cracking up but does as he's asked* "That was priceless! The look on your face!"**

**NekoShard: "Come on! You know I just watched "Silence in the Library" and that I have an overactive imagination! Don't do that to me." **

**Raph: "Heh, sorry Neko. Let's get on with the story to take your mind off the scare."**

Nightshade stood a little behind Bishop, his eyes flicking around the room, identifying all possible threats. Many robotic ninja crouched in the shadows, the red glow of their eyes betraying their presence. A fish mutant with robotic legs guarded the door looking very bored. Next to him stood a large turtle with a black mask. He had an evil gleam in his eyes as he surveyed the room and hefted a heavy mace onto his shoulder. Upon the dais in front of him and Bishop was a large stone throne upon which lounged a girl who looked to be about sixteen. She wore dark ninja clothes and a polished silver breastplate. Her black and blond hair combined with the heavy red and black eye makeup gave her a look of danger and power. Behind the chair lurked a large, wolf-like figure, it's red eyes fixed un-blinkingly on the dark turtle.

Gritting his sharp teeth, Nightshade swished his armored tail across the floor restlessly as the girl on the throne sat up and said in a cutting voice.

"Your late Bishop. You promised the merchandise by the end of last month and you are three weeks overdue. Explain."

Bishop's face remained impassive as he replied. "I had every intention of sending it on time. However, good things come to those who wait, and I feel certain that Nightshade will be well worth the delay. He is eager to prove himself and to rid this city of your enemies."

The girl sighed, "Come forward."

Obeying, Nightshade stepped up to the foot of the dais and dropped to one knee to show his respect.

"What reason do you have for serving me faithfully?"

"Let's just say, I have a few loose ends that need to be tied up here," raising his head, Nightshade allowed his yellow-gold eyes to stare defiantly up at the girl. She glared back, narrowing her eyes. Then they widened and she gave a slight gasp.

"Bishop! I need to speak with you in private."

"Of course, Karai," the scientist followed the kunoich into a room through a door behind the throne.

As soon as they had left the room, the other mutants converged on the newcomer.

"So, we have another turtle coming to join us," The fish said in a smooth, accented voice.

The huge turtle stumped over and squinted down at Nightshade. "He looks more like a lizard to me. What turtle has a tail that long?"

"He certainly doesn't look like a warrior," growled the wolf/dog mutant. "He doesn't even have a weapon."

Without warning, Nightshade struck out with his tail. The weight of both muscle and armor knocked an unprepared Rahzar off his feet. The other turtle swung his mace, and Nightshade stepped casually out of the way, his eyes gleaming with the light of battle. The mace struck Rahzar on the forearm as he was pushing himself to his feet and he fell back once more with a howl of rage and pain. The fish mutant took Nightshade's momentary distraction to lunge forward, jaws gaping and ready to sink their venomous fangs into his shoulder, but Nightshade turned quickly and threw up his right arm to defend himself. Fishface's teeth ricocheted of the lightweight, but solid steel that made up the bracers that covered the dark turtle's forearms.

The three mutants prepared to attack again, but a voice cried loudly,

"_STOP!"_

Immediately, they backed away from Nightshade, shooting him loathing glances. Karai walked towards them and said coldly, "I will not have you killing the newest member of the Foot Clan. Especially now that I see he has far more skill than any of you bumbling freaks."

Bishop exited the room without looking once at Nightshade as Karai tossed her new assassin two pieces of dark fabric. Catching them, he saw that one was a cloak made from a material that was such a dark shade of purple that it was nearly black. The second was a mask of the same material.

At a gesture from Karai, a Foot Ninja moved forward and offered a black bundle to the new recruit. Accepting it, Nightshade unwrapped a stunning scythe. It was made entirely of dark metal and razor sharp. The blade was a smooth curve, but along the top it became slightly serrated, allowing for it to tear through armor. The long handle was wrapped in smooth black leather to make it easier to grip and the overall impression was that the weapon was one of extreme danger and power. Driven by an instinct, Nightshade raised the weapon and spun it as one would a staff, tilting it slightly upward in order to compensate for the extra weight on the end of the shaft. He then planted the butt of the weapon firmly on the ground and knelt before Karai, awaiting his orders.

"Bishop sent some soldiers to me before he brought you here," informed Karai. "You will lead them for me. Now go and take command before you rest. I will have need of you tomorrow."

Nightshade lowered his head, "Of course, Karai."

A figure came up to the assassin and beckoned for him to follow. As they left the dark throne room and entered a bright hallway, Nightshade realized that his guide was a girl who looked to be about fifteen. She had green, scaly skin and a tail that was nearly as long as his. She wore black shorts and a black t-shirt that stopped right above her stomach as well as black wrappings on her feet. Her eyes were a dull brown and she had grey-green hair pulled back into a low ponytail.

"What is your name?" Asked Nightshade. The girl looked at him and said in a clipped tone,

"Iranie. I am to be your second in command. It is me you had to meet; the other troops will obey you without question. The only reason I was put in charge was because some glitch in the system that created me and the others gave me a higher intelligence level."

Iranie drew to a stop before a door and said shortly, "This is your room. If you need me, I'll be bunking on the lower levels with the rest of the clones."

Nightshade nodded and entered the room. He strode over to the mirror that hung on the wall, and gazed at his reflection. His mouth curved into a wicked smirk as he thought of how sweet his revenge would be.

**NekoShard: **_*****__**Evil laugh**__*** "Oh yes I did enjoy this! I am sorry, but writing about evil is just so…fun."**_

**Raph: **_**"And the others call me twisted!"**_

**NekoShard: **_**"It takes one to know one…"**_

**Raph: **_**"Now wait a minute-"**_

**Leo: **_**"While those two fight it out I will close this conversation. Please review everyone! ***__**Smiles at the fans**__*****_


	9. Chapter 9

**NekoShard: **_**"Hey everyone, sorry that this chapter took longer to put up! I was on writer's block for a little while."**_

**Raph: **_**"Aw don't sweat it! I do things late all the time and everyone loves me!"**_

**NekoShard: **_***Sigh* "I hope you enjoy this chapter! I was up till freaking 5:15 a.m. to get it done and up!"**_

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

"BOOYAKASHAAAAAAAA!"

The sharp blade of a kusuragame sank into the metal skull of a Kraang robot and the object collapsed as the squishy pink alien clambered out and scurried into a dark alley. Yanking the weapon free, Mikey reverted it back to its nunchuck form and twirled it above his head before bashing another robot, sending it flying back onto Leo's blades. Grinning, Leo gave his little brother a thumbs up before turning away and slashing another robot into pieces. Raph was like an avalanche of destruction, none of the Kraang that stood in his way remained in one piece. He relished the opportunity to let out his pent up anger and wasted none of it.

The fight was over quickly. Robots lay lifeless on the ground, their limbs scattered about as the three brothers surveyed their work with satisfaction.

"Nice work guys," Said Leo as he sheathed his blades. "The Kraang didn't stand a chance."

Raph grinned and spun one of his sai as he said, "When have they ever stood a chance?"

Cheerfully, Mikey slapped Raph hard on the back and laughed at his elder brother's words. The jolt caused the red-masked ninja to lose his grip on his weapon and it flew from his hand, skidding into the alleyway that the Kraang Mikey had attacked had run down.

"Smooth…" laughed Mikey. Raph scowled, looking more like his old self before stomping after the weapon, vanishing into the shadows. A moment later, Raph came flying out of the alley and crashed into a lamppost. He sat up quickly yelling,

"ACK! Get it off!"

His brothers ran over and burst out laughing. The same Kraang that Mikey had chased off was now latched onto Raph, it's tentacles wrapped firmly around his face as it stared back at the alley from whence it came, its eyes wide in apparent terror.

Mikey was on the ground, holding his side as he choked out, "Dude, how did you get that thing attached to you? You two look so stupid!"

"I didn't," Raph growled, his voice faintly muffled by a pink tentacle. "It just came flying at me from the shadows and grabbed on! Now stop laughing and get it off me!"

Still sniggering, Mikey began prying the alien loose. Raph looked over at where Leo stood with his back to them and said,

"What, you to important to give me a hand with this?"

Leo shook his head, not turning to face his brother as he muttered out of the corner of his mouth: "Don't show any signs of alarm, but we are being watched."

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

**Earlier that night…**

Nightshade was preparing himself to go on his first mission. He strapped on his dark purple shoulder armor that reached down his upper arm, the sturdy, multi-segmented tail armor, and black pants that could help disguise his species somewhat. Flinging the cloak about his shoulders and pulling the hood up to shroud his features in shadow, the assassin picked up his scythe and strode into the throne room. Karai was still reclining on the large chair, and as he passed Xever he heard the mutant mutter to Slash,

"I don't see why we have to take orders from a stuck up teenager, even if she is the Shredder's daughter!"

Casually, Nightshade set the edge of his blade against Xever's throat and hissed, "I'd watch your words if I were you; you never know who might be listening."

Xever swallowed nervously, and gave a slight nod, his eyes full of loathing. Retreating, Nightshade strode down the walkway to kneel before Karai.

"You called?"

Sitting up straight, Karai smirked slightly as she said, "Yes, I did. I need you to take your warriors out onto the rooftops and patrol for the Turtles. Report to me on your findings."

Standing, Nightshade bowed and turned to leave. As he reached the door, Karai called out as if in afterthought, "Feel free to rough them up all you want. Just make sure they survive so I can get my revenge later."

A pointed smile flickered at the corners of Nightshade's lips as he climbed to the top of the building and summoned his troops, twenty in all. They assembled silently and obediently. Iranie was at the fore and she bowed formally to her commander. He surveyed the clones, noting that Iranie appeared to be the only female, before dividing the group in half and ordering them to spread out over the city, and to radio back their findings. Iranie left with her group and the other warriors left as well. Nightshade breathed in the scent of the night air before fading into the shadows and dashing across the rooftops. He wanted to find the Turtles himself, once he did so he would send the clones back and deal with those traitors himself. He paused for breath near an empty park and gazed up at the starlit sky. A faint noise came to his attention and he turned to look down the street. Three green figures were running and leaping, slashing at other forms. Nightshade immediately felt energized and began to make his way down to where the fight was. He watched his former brothers carefully, learning their moves. The orange masked one seemed pretty reckless and not much of a threat to him, the blue one appeared to be the eldest and was a more formidable fighter, but his attacks were rehearsed and predictable. Then Nightshade's eyes fell on the final turtle and his eyes narrowed in anger. This one was a far more dangerous enemy, he fought skillfully but no two moves were ever alike. The dark turtle's eyes were fixed on his weapons, a pair of sai blades, and one hand crept up to feel the edges of the scars that marred his face. Suddenly, he whirled around and held his scythe to the throat of a figure who had crept up behind him, only to remove it a second later as he realized the person was his second in command.

"What are you doing here?" He snarled, "I told you to remain wit your squadron."

Iranie's face remained impassive as she replied dully, "We found nothing. I sent the other clones home and came for you. It is my duty as second in command."

The clone glanced down as the fight below them came to a close before leaping down into the alleyway. Nightshade opened his mouth to order her back to the rooftops but shut it again as she picked up a brain-like creature and began running her blade lightly over it, not drawing blood, but toying with is as a cat would with a mouse. A clattering noise sounded as a sai blade skidded into the dark alley. Moments later, the red-masked ninja stalked in and bent to retrieve it. Nightshade clenched his hands into fists at the carelessness of Iranie. Any moment now the turtle would straighten up, see her, and their whole advantage would be gone. Just as the ninja stood up, Iranie flung the Kraang away from her bored. It screeched, hit the turtle's face, and clung to it tightly. The mutant yelled in terror and dashed from the alley. Nightshade made use of the distraction the dash across the power lines to the opposite buildings. The orange ninja was helping pry the alien off of his brother's face, laughing the whole time. The eldest however was gazing up at the roof Nightshade had just left. Following his gaze, the assassin saw that Iranie was standing at the edge looking down. He silently cursed Bishop and Karai for not training their warriors better but continued to watch. He heard the older brother say to the others.

"Don't show any signs of alarm, but we are being watched."

Immediately, Nightshade climbed off the building and into the alley directly behind them and watched as the red turtle tossed the alien aside and stood up casually, but the orange one immediately gasped and shrieked in horror.

"It must be Cottage Cheese Demon! The Kraang must have brought him back as a zombie and now he is coming to get revenge and eat our brains! OH MY GOSH WE'RE ALL GONNA DIE!"

The tough turtle snorted derisively, "Relax Mikey, your imaginary zombie cheese demon wouldn't go after you. He wants to eat, not diet."

"Stop talking you two!" Snapped the blue-masked turtle.

"Geez Leo…" muttered the red turtle.

The one called Mikey swallowed hard and backed up slightly and Nightshade made his move. Deciding not to use his scythe at close quarters, he took out a wicked looking knife and clapped a hand firmly over Mikey's mouth, holding the blade to his throat.

Mikey opened and closed his mouth several times before squeaking out,

"Raph…Leo…"

"Wait a moment Mikey," replied Leo as he looked up at where Iranie stood watching them.

"This is really important!"

"Just a sec…"

"Raph…please…"

With a sigh, the red turtle, Raph, turned to look at his younger brother and let out a yell of anger and surprise, causing Leo to whirl around in alarm as well. Nightshade smiled cruelly at their dismay and said,

"Drop your weapons, or your brother will be able to breath out of his neck."

Leo and Raph just tightened their grips. Nightshade's sneer widened and he pressed the knife even more firmly against his prisoner's throat. He could feel the younger turtle trembling and felt a cold satisfaction.

"I said, drop your weapons."

Slowly, Leo laid his weapons on the ground; Raph angrily did the same. Nightshade relieved the pressure slightly and said cuttingly,

"I'm surprised you complied," directing his next words at Mikey he continued. "I wouldn't expect to be around much longer with these two. You're painfully stupid. They'll want to get rid of you as a weak link. It wouldn't be the first time."

Mikey wimpered in fear and Raph growled, "Let him go. We dropped our weapons didn't we? What more do you want?!"

Nightshade shrugged slightly, curling his tail around Mikey's ankle, causing him to squirm.

"I suppose you did. Catch."

He shoved Mikey forward roughly. Leo and Raph caught him before he hit the ground, his legs shaking so hard that they barely supported him.

"This was just an introduction. From now on, never assume the shadows to be your allies. I'll be watching and waiting, relishing every opportunity to cause you pain."

He began to back into the alley but paused and spun his knife casually,

"Don't worry, I'll leave you a parting gift."

With lightning speed, he flung the knife at Raph. The Turtle didn't even have time to move before the long knife pierced his upper arm, burying itself to the hilt and the tip of the blade stuck out the back. Raph fell to the ground with a cry of pain as blood coated his arm and hand.

Nightshade melted into the shadows as he murmured, "Lest you forget me…"

While the others clustered around their brother, Nightshade climbed to the top of the roof and signaled for the female clone on the opposite roof to return to the Foot Clan's headquarters with him. The thrill of revenge coursed through his veins and his yellow eyes shone with triumph.

Raph gritted his teeth at Leo pulled the blade out of his arm and Mikey used Raph's mask as a bandage along with his own.

"Guys, I think this guy is worse than Cottage Cheese Demon…" He said in a small, frightened voice.

Raph smiled slightly and managed to stand, retrieving his weapons and sheathing them in his belt as he looked at his older brother.

"Who was that guy? Did you see his face?"

Leo shook his head slowly, and his hands clenched angrily as he replied,

"No. But whoever he is, he's not going to get away with his threats. Not if I have to kill him myself."

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

**NekoShard: **_**"And thus we begin to see a darker side to Leo!"**_

**Raph: **_**"I always knew it was there." *Grins at the reviewers* "Hey, the first five people to review get a personal shout out from yours truly here."**_

**NekoShard: **_**"You shameless flirt…"**_


	10. Chapter 10

**Raph:**_** "Yo **__Write Renee Write; Skscatluna__**! *Fistbump* Hey **__JustineElla2__**, **__MistDust23910, Taro the hedgehog, __**high three!**__ *__**Grins***_

**Mikey: **_**"Awwwww Raphie's making friends! I'm so proud of you!"**_

**Raph: **_**"Why you little… *Moves to hit Mikey***_

**NekoShard: **_**"Hey, knock it off you two! You're going to miss the next chapter."**_

"Leo will ya stop acting so worried about me? I'm fine!"

April looked up from her homework to see Leo supporting Raph while Mikey tagged along behind them, casting nervous glances over his shoulder as he went. She got up quickly in alarm at the sight of Raph's bloody arm.

"Guys! What happened? Raph are you alright?"

The wounded mutant finally succeeded in shrugging off his brother's helpful hand and shrugged, "It's nothin', just a scratch."

"More like a full blown knife through your arm," Snorted Leo as he walked towards the dojo to get Master Splinter. "You need to get that cleaned out and bandaged, maybe even some stitches."

Raph rolled his eyes, but allowed April to lead him to the couch. Suddenly, he looked over at Mikey and said,

"How's your throat?"

Mikey forced a grin, "Just fine bro, can't even feel it anymore."

"Throat?" Asked April in alarm. Mikey tipped his head back, revealing a long, thin red line that stood out brightly against his green skin.

"My sons, what happened?"

April and her friends turned around to see that Master Splinter had entered the room, Leo trailing behind him and carrying a large wooden box.

"I was about to tell you, Sensei. We got attacked by some mysterious mutant while topside! He grabbed Mikey and threatened to slit his throat if we didn't drop our weapons."

"And did you?" Asked April.

Raph nodded, wincing slightly as Splinter began cleaning the wound with a solution from the chest Leo had been holding.

"I thought he was going to tie us up or something, but he just said this was an introduction, shoved Mikey back at us and stabbed me through the arm before escaping-OW!"

The others looked at Raph in surprise, he hardly ever showed he was hurting, but now he had his head in his hands, eyes screwed shut in pain.

"Raphael," Splinter said gently. "What is wrong?"

Sitting up straight, Raph looked confused. "I don't know…my head just started to hurt a lot and I felt really-really sad…But it's gone now, I feel just fine!"

Master Splinter said nothing, but he looked concerned as he finished wrapping fresh bandages around his hot-tempered son's arm.

"You will need stitches, but I do not have the right thread. April, will you purchase this for me?"

April bowed politely, "Of course Master Splinter! I'll be right back."

Nightshade paced the back of the throne room. Karai was somewhere in a meeting with the Kraang and he had nothing to do. The other mutants were steering clear of him, partly from fear and partly because they disliked him. His tail lashed restlessly and he had to struggle not to strike out at the first FootBot he came across with his weapon. That would not go over well with Karai.

Karai…Something about her gave Nightshade the feeling that she knew more about him than she was letting on. Maybe it was the way she looked at him with mingled curiosity, wariness, and hatred. But he was probably over reacting. They had only just met, she couldn't know any more about him than he himself had told her! Shaking off the thought, Nightshade made up his mind to go outside. He stalked past Xever and out into the open night air, climbing swiftly to the top of the church they hid in and began leaping from one roof to another, not really looking to go anywhere in particular, but to simply let out some pent up energy. He did not pay attention to where exactly he was going, but he suddenly skidded to a halt at the edge of one of the buildings. He was on, well, above, main-street. Looking down, he saw the pharmacy and watched as a few people drove by in cars or walked their dogs down the sidewalk. A female figure in a yellow shirt with her red hair pulled back in a low ponytail exited the pharmacy, her head down as she counted her change and walked down an alleyway. Bored, Nightshade was about to turn away, when he noticed three shady looking men slink down the alley after the girl. A switchblade gleamed in the leader's hand. A mugging. Nightshade gave a noise of distaste and leaped to the opposite roof before glancing down and listening to the words being exchange. The girl had just realized that she'd gone down a passage that led to a dead end. She turned to exit the passage, but stopped short as she saw the men approaching her.

"Hand over the money, and no one gets hurt," commanded the thin one who seemed to be the leader. The girl glared at him and reached for something in her back pocket, but the bigger man grabbed her arms and held her still.

"End of the line sweetheart," smirked the man with the knife. He moved forward and Nightshade leaped from his perch on the roof to the ground below. He landed lightly and unsheathed his scythe.

"I really wouldn't do that if I were you," he said coldly. The men whirled around in surprise and alarm, their faces hardening into expressions of anger.

"Stay outta this, freak! It ain't your business."

Lunging forward, Nightshade swept the mugger's legs out from under them. The larger man tried to support himself by grabbing the girl, but only succeeded in dragging her down with him. Nightshade casually shouldered his weapon and smirked,

"Now it is."

The leader jumped to his feet and ran at him, slashing wildly with the knife. He was clearly a bit drunk and not at all coordinated in his attack. The other men joined him, the large one throwing the girl to the side so she stumbled hard into a wall. Nightshade didn't have time to see if she was alright as he was in the middle of combat. The fight didn't last long, the Foot Assassin dispatched two of the thugs with a single sweep of his tail and sent the leader flying out of the alley with a well aimed jab from the butt of his scythe. The man groaned and got unsteadily to his feet and staggered away down the street slurring, "This ain't over lizard!"

Turning back to the red-head, Nightshade's night vision kicked in and allowed him to see her features properly for the first time. She had large blue eyes with long lashes, light skin with a cute splash of freckles across her nose and cheeks. Her red hair shone in the faint light. Nightshade's eyes widened and he felt a blush rising on his face, making him glad that the hood would hide his features. He took a step forward, only to jerk his arm up to shield his face as something sharp and flat flew towards his face. It was deflected off his arm guard but the momentary distraction allowed the girl to race past him and out of the alley, escaping. Nightshade gave a faint snort of annoyance, and turned to pick up the weapon. His eyes showed slight surprise when he saw that it was a fan, a _tessen_, commonly used by kunoich. At the center was a simple, circular symbol. It seemed slightly familiar…

"…And then he knocked them into the street and they ran off. I threw my fan at him to distract him, and ran for it."

April recounted her adventure to her friends back in the lair, all of whom listened eagerly.

"That guy has some nerve to be out causing trouble twice in one night," muttered Leo.

Master Splinter nodded slowly, "I agree Leonardo, but if he were not, April might have been injured or violated. He cause no trouble for us in this case."

April looked down embarrassed, "I lost my weapon though. I'm sorry Sensei, I'll go looking for it tomorrow."

"All that matters right now is that you are safe, April. The fan was a possession, and I value your life more."

Smiling, April stood up to leave. Raph looked startled,

"You can't seriously be going out! What if that freak comes after you again?"

"I don't have much of a choice," said April with a slight shrug. "I promised my aunt I'd be home by ten and I have school tomorrow. Don't worry, I'll be fine. See you tomorrow!"

Later that night, April was finishing her French homework in bed when a shadow flickered in the corner of her vision. She turned quickly to look at the window, but what ever had been out there was gone now. Opening the window slightly, April's eyes widened in surprise. Laying on her windowsill was her tessen! As she picked it up, she noticed a note underneath it. Written in thin, slanted handwriting were the words: _You forgot something._

Nightshade watched from the roof directly across from April's house as the redhead went back inside. Moments later, the lights went out in her room. With a sigh, the dark turtle sank down with his back against the wall. He felt so strange.

"Why is my heart pounding so fast, and why is my face getting warm?" He wondered, looking up at the cloudy sky. "What's the meaning of this?"

**Raph: **_**"What's with Donnie? He may be clueless about a lot of things, but her certainly knows when he's in love!"**_

**NekoShard: **_**"That's just it. When Bishop removed some brain fluid he didn't just destroy Donnie's memories, he also destroyed Donnie's ability to understand/remember any feelings of love of companionship. He only knows about hate, revenge, anger, and sadness."**_

**Raph: **_**"So let me get this straight. Donnie is in love with April but he doesn't know that he loves her? This should be fun to watch so please review everyone!"**_


	11. Chapter 11

**Casey: **_**Yo Neko!**_

**NekoShard: **_**"What did I tell you about coming in without knocking, Jones?"**_

**Casey: **_**"You told me not to."**_

**NekoShard: **_**"Soooo…"**_

**Casey: **_**"Aw come on kitty-cat! Do I look like someone who does what he's asked?"**_

**NekoShard: **_***Sigh* "Fine. Just stay quiet until this is done."**_

"What do you mean they escaped you?!" Karai shrieked at Nightshade where he knelt before her. "Bishop told me you were the best assassin of the lot, how could you have failed to bring those mutants to me?"

Nightshade raise smoldering gold eyes to look at the Shredder's daughter as he said coldly: "There is a difference between killing an enemy from a distance or in the shadows, and tying them up to drag back as your captives. It was a three to one fight and I did the best I could under the circumstances. I managed to injure the strongest one so that he will only be able to use one arm for a while now, which is better then what you have accomplished thus far."

Karai scowled and stood up so that she could look down on him even more. "Perhaps. But you still failed me and I don't forget something like that easily."

She turned away and looked over at Iranie who was lurking in the shadows, her face as blank as ever.

"Your second in command will lead the clones for now. I want you in charge of the FootBots, they seem more your speed."

Making an effort to suppress his anger, Nightshade muttered, "Your wish is my command, daughter of Shredder."

Karai laughed softly, "Yes, it is."

She made a dismissive gesture, indicating that Nightshade could leave. The mutant left the room at an even gait, but once he was outside and on the roof, it turned into an outraged stalk. To be put in charge of those inferior robots, those pathetic excuses for ninja, was humiliating! With a growl of anger, Nightshade lashed his tail, taking out a satellite dish. He watched as it shattered before turning away and on to the next building; someone was going to be without cable TV for a while. A fight was what he really needed, something that allowed him to let his anger out in an acceptable environment.

At that moment, he heard noise from the alleyway in front of him. He moved forward and looked down. Two figures were fighting, one a teen in a hoodie and ghoulish mask armed with hockey pucks and sticks. The second was the red-masked turtle Raphael, his sai blades gleaming as he deflected a well-aimed hockey puck before it hit him between the eyes.

_ "This might prove interesting."_ Thought Nightshade as he watched the two other teens fight their way into the street. A chase soon followed, but the human was eventually overpowered and flung onto the hood of a parked taxi. Raphael raised his sai and drove it towards the other fighter's face, stopping an inch short. He shook his head slightly as if he were trying to clear his head.

"What am I doing? Maybe I do have anger issues-_ACKZZzzzzzz!_"

The human had somehow electrocuted his opponent with some sort of stunner concealed in his bulky glove before grabbing on to a passing car, allowing it to drag him away with a parting shout of: "This ain't over freak!"

"Yeah?! You'd better run, or skitch! _Whatever!_"

Nightshade watched as the battered turtle glanced quickly around before stooping to move a manhole cover and leaping down into the sewers.

"So that's where you live…excellent. You'll lead me straight to your home."

Nightshade didn't tell Karai of his plans, not wanting her to get involved and steal his glory, but every night he watched for the the turtle so that he could follow him. On the third night, he and his robotic soldiers were crouched in the shadows on one roof, when a loud crash drew his attention. He dashed three roofs over and looked down just in time to see Raphael go down into the sewers. Nightshade was about to give the order to follow when he saw the same masked teenager follow the other turtle. He cursed under his breath, but gave the order to follow. He landed on the floor of the sewer in a crouch. Over that past week or so he had become much more graceful and had fully adjusted to his new body. As he dashed through the sewers, he revelled in the strength speed with which he moved and at the same time the perfect silence. His eyes could see in the dark as clearly as they could in broad daylight, and his more sensitive hearing enabled him to follow the two teenagers only by the sound of their breathing. Not that he needed to, Raph was cursing and complaining about his brothers loud enough to wake the dead. As he slipped through the shadows, he saw that they had exited the sewer lines and were now on an abandoned subway track. Leaping onto a support beam, Nightshade followed them from above, his warriors directly behind him. He watched for a moment as Raphael entered his home and the masked teenager tried to sneak over for a better view, knocking over some boxes and alerting them to his presence. A short struggle ensued and he gestured for the FootBots to move in silently, which they did. He smirked, about to give the signal to attack, when a glimpse of yellow and red out of the corner of his eye. His head whipped around to stare in surprise. It was the same red haired girl he had helped several nights before.

"What's she doing here?"

She was talking with the four other teenagers but then she clutched her head.

"Sensei! We're not alone."

She looked up at the FootBots and the others followed her gaze, but Raphael turned to stare directly where Nightshade crouched in the shadows. Deciding the time for conceilment was at an end, he jumped to the ground, and shouted, "Foot Clan, Attack!"

Chaos erupted in the lair and the air was filled with sparks, weapons, and robotic limbs. Nightshade was in the thick of the action, always aiming for Raph whenever possible. He paused for a moment and grabbed the nearest robot. "Remember this location and go inform Karai!"

The robot bleeped twice, it's eyes glowing, and then dashed away.

"After it!" Called the rat master. Raphael and the masked human teen raced away.

"Casey Jones is on it!" "Tell Casey Jones I don't need his help!"

Turning, Nightshade threw up and arm only just in time to block a blow from Leonardo. He smirked, his gold eyes shining at the blue ninja with the light of battle.

"So we meet again, Leonardo."

Leo narrowed his eyes and leaped back, only to lunge again. "You know our names, but never told us yours. Who are you?"

The dark turtle's eyes flickered with uncertainty for a moment as he remembered the same question being asked him once before. But his eyes hardened and he pressed his attack more forcefully.

"Names have power, but they can also stand for something. Mine is Nightshade; let it strike dread into your heart whenever you hear it uttered!"

Shaking his head, Leo snarled, "I've faced worse fears than you!"

He swung his swords, trying to slice his opponent's throat, but Nightshade sidestepped easily. "I've been watching your moves, your technique is painfully obvious!"  
Throwing a ninja star, Leo crouched and swept Nightshade's legs out from under him. "Was that painfully obvious, or just obviously painful?"

With a growl, the assassin leaped to his feet and lashed Leo across the plastron with his powerful tail, sending him reeling back. Whirling his scythe, Nightshade struck at Leonardo. The blow never hit him. Unable to prevent the attack completely, Splinter had knocked his son out of the blade's path and was struck instead. He didn't make a sound as he collapsed against the wall. Nightshade's eyes widened in surprise, and it seemed that everyone in the lair froze in place, all staring at where he stood over the fallen ninjutsu master. Mikey's scream broke the silence.

"SENSEI, NO!"

The Foot immediately formed a barrier between their commander and the enemy, but Leo managed to break through a weaker part.

"I'LL KILL YOU, YOU MONSTER!"

Nightshade began to back up, desperately trying to block the insane, powerful sword strikes with his scythe. Tears were welling up in Leo's eyes, as he fought harder than he ever had before. Swiping with his tail, Nightshade attempted to knock Leo back again, but his opponent was prepared. Ducking and summersaulting, he avoided the tail and stood, swinging his blade as hard as he could. It cut straight through Nightshade's tail and armor, severing the limb completely in half. Nightshade arched his back with an agonized scream as blood poured from the wound. He staggered away from where Leo crouched by his tail. Glancing around, he saw that the last of his troops had been defeated. Shaking with pain, he turned and dashed away, escaping the sewers and leaving a trail of blood behind him. Leo made a move to go after him, but a weak voice called, "Leonardo. Let him go."

Leo turned back just as Raph and Casey returned. There grins faded to expressions of concern and horror as they clustered around Splinter.

"Go get the medical supplies, we're going to need a lot of bandages-"

"-if we're going to stop this bleeding." Stockman finished ordering Xever. Nightshade clenched his hands to stop himself from throttling the nervous wannabe villain.

"You're services are not required for this, Stockman." Karai said from the door. She walked over and gestured for him to leave, which he did, looking relieved. Facing Nightshade, she said.

"Bishop gave me some information about you. You apparently were joined with some lizard DNA and it lets you regrow your tail. It will take about three days, but you cannot bandage it. You have to let the blood drain and clot on its own."

Karai turned to leave, but added. "You'll be put back in charge of your original troops, your second in command nearly got them all killed. We'll discuss exactly how you received these injuries at a later time."

Sitting alone, Nightshade stared dully at the wall. He had killed the rat, causing great pain to his brothers like he wanted. "So why did that hurt so much…?"

**Casey: **_**"Woah…Raph said you went off the deep end, but I didn't think it was this bad!"**_

**NekoShard: **_**"Oh, he said that did he?"**_

**Casey: **_**"Um, Hey look you only need five more reviews before you reach a hundred! Haha…why don't you focus on that while Raph and I esc-"**_

**NekoShard: **_**"Nice try puck-head. Get back here you!"**_

**Casey: **_**"Aw geez no! RAPH RUN NEKO'S ON THE RAMPAGE AGAIN!"**_


End file.
